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<p>The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC<sup>HHS</sup>, a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC<sup>HHS</sup> captures &gt;95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at &lt;0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC<sup>HHS</sup> isolate&#xa0;genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC<sup>HHS</sup>, its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.</p>

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Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年5月25日

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  • Uyen Thy Nguyen,
  • Rauf Salamzade,
  • Shelby Sandstrom,
  • Mary Hannah Swaney,
  • Elizabeth C. Townsend,
  • Sherrie Y. Wu,
  • J. Z. Alex Cheong,
  • Joseph A. Sardina,
  • Isabelle Ludwikoski,
  • Mackinnley Rybolt,
  • Hanxiao Wan,
  • Caitlin M. Carlson,
  • Jordana Ferro,
  • Owen McArthur,
  • Won Se Suh,
  • Robert Zarnowski,
  • David R. Andes,
  • Cameron R. Currie,
  • Lindsay R. Kalan

摘要

The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPICHHS, a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPICHHS captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPICHHS isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPICHHS, its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.